Variant rs11564258 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_173600.2(MUC19):c.85+587G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0328 in 152,266 control chromosomes in the GnomAD database, including 231 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.033 ( 231 hom., cov: 32)

Exomes 𝑓: 0.013 ( 0 hom. )

Consequence

MUC19
NM_173600.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.722

Variant links:

Genes affected

MUC19 (HGNC:14362): (mucin 19, oligomeric) This gene encodes a member of the gel-forming mucin protein family. Mucin family members are glycoproteins that have tandem repeats which are extensively O-glycosylated. The structural features of mucin proteins are responsible for the gel-like properties of mucus. The encoded protein may be involved in disruption of the ocular surface in Sjogren syndrome. [provided by RefSeq, Apr 2014]

MUC19 links:

ENSG00000258167 (HGNC:):

ENSG00000258167 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.113 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Protein	UniProt
MUC19	NM_173600.2 link	c.85+587G>A	intron_variant	NP_775871.2	Q7Z5P9-1
LOC105369736	XR_007063562.1 link	n.305-2512C>T	intron_variant
LOC105369736	XR_944866.1 link	n.409+62C>T	intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	Protein
MUC19	ENST00000454784.10 link	c.85+587G>A	intron_variant	5	ENSP00000508949.1
ENSG00000258167	ENST00000552757.1 link	n.222+62C>T	intron_variant	5
MUC19	ENST00000676020.2 link	n.138+587G>A	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.0328

AC:

4990

AN:

152068

Hom.:

230

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00770

Gnomad AMI

AF:

0.0526

Gnomad AMR

AF:

0.117

Gnomad ASJ

AF:

0.0582

Gnomad EAS

AF:

0.0398

Gnomad SAS

AF:

0.107

Gnomad FIN

AF:

0.0290

Gnomad MID

AF:

0.0886

Gnomad NFE

AF:

0.0218

Gnomad OTH

AF:

0.0440

GnomAD4 exome

AF:

0.0125

AC:

AN:

Hom.:

AF XY:

0.00

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0156

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.0328

AC:

4996

AN:

152186

Hom.:

231

Cov.:

AF XY:

0.0365

AC XY:

2713

AN XY:

74398

show subpopulations

Gnomad4 AFR

AF:

0.00768

Gnomad4 AMR

AF:

0.118

Gnomad4 ASJ

AF:

0.0582

Gnomad4 EAS

AF:

0.0397

Gnomad4 SAS

AF:

0.108

Gnomad4 FIN

AF:

0.0290

Gnomad4 NFE

AF:

0.0218

Gnomad4 OTH

AF:

0.0435

Alfa

AF:

0.0279

Hom.:

142

Bravo

AF:

0.0390

Asia WGS

AF:

0.0860

AC:

297

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.21

DANN

Benign

0.36

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over